SRM proteomics

Expression dataThe abundance of endogenous peptides is quantified as a ratio to spiked-in synthetic peptides containing stable heavy isotopes and log2 transformed. During normalization, the “light/heavy” log2-ratios for each sample are shifted such that the median is set to zero.

Signal-to-noise assessmentAfter homogenization, small aliquots from each of the samples are pooled together and scattered throughout the study (8 samples per 96-well plate) to help capture variance that is due to sample preparation steps (except homogenization) and instrumental measurements. The standard deviation across controls indicates precision of the measurement. The signal-to-noise ratio is calculated as the ratio of variance across human subject samples vs. pooled controls. If the variance across the controls is equal to or higher than that across the human subject samples, the peptide is discarded from further consideration.

Handling redundancyIn most cases, the correlation was significant, and the peptide with the best signal-to-noise ratio was selected. However, some proteins were measured with multiple peptides. APP was measured with 4 peptides: 2 targeted at the core APP sequence, bA, and bA38. MAPT or tau was measured with 2 peptides targeted at tau_AT8 and tau_AT8_s202. Further details can be found in the data dictionary.

The data set includes the following proteins:

AK4

Adenylate kinase 4

ANKRD40

Ankyrin repeat domain 40

AP2A2

Adaptor-related protein complex 2 alpha 2 subunit

APOE

Apolipoprotein E

APP*

Amyloid beta precursor protein

bA*

Beta Amyloid (APP)

bA38*

Beta Amyloid (APP)

BCL2L1

Bcl-2-like protein 1

BIN1

Bridging integrator 1

C1QA

Complement C1q subcomponent subunit A

CD2AP

CD2-associated protein

CD44

CD44 gene

CD47

CD47 gene

CPLX2

Complexin-2

DOCK2

Dedicator of cytokinesis 2

FBXO2

F-box protein 2

FCER1G

Fc fragment of IgE receptor Ig

FYN

Proto-oncogene, Src family tyrosine kinase

GSTP1

Glutathione S-transferase pi 1

HSPB2

Heat shock protein beta-2

IGFBP5

Insulin-like growth factor-binding protein 5

ITPK1

Inositol-tetrakisphosphate 1-kinase

KIF5B

Kinesin family member 5B

MEF2C

Myocyte enhancer factor 2C

PADI2

Peptidyl arginine deiminase 2

PICALM

Phosphatidylinositol-binding clathrin assembly protein

PLXNB1

Plexin B1

PVALB

Parvalbumin

SASH1

SAM and SH3 domain-containing protein 1

SLC6A12

Solute carrier family 6 member 12

SNAP25

Synaptosomal-associated protein 25

SNAP29

Synaptosomal-associated protein 29

SNAP47

Synaptosomal-assocaited protein 47

SNCA

Alpha-synuclein

STX4

Syntaxin-4

STX5

Syntaxin-5

STX7

Syntaxin-7

STX12

Syntaxin-12

STX16

Syntaxin-16

STX18

Syntaxin-18

STX1A

Syntaxin-1A

STX1B

Syntaxin-1B

STXBP1

Syntaxin-binding protein 1

STXBP3

Syntaxin-binding protein 3

STXBP5

Syntaxin-binding protein 5

STXBP6

Syntaxin-binding protein 6

SV2B

Synaptic vesicle glycoprotein 2B

SYN1

Synapsin I

SYN2

Synapsin II

SYN3

Synapsin III

SYT1

Synaptotagmin-1

SYT2

Synaptotagmin-2

SYT7

Synaptotagmin-7

SYT11

Synaptotagmin-11

SYT12

Synaptotagmin-12

TARDBP

TAR DNA-binding protein

tau_AT8*

Microtubule associated protein tau (MAPT) or tau

tau_AT8_s202*

Microtubule associated protein tau (MAPT) or tau

TRIM28

Tripartite motif containing 28

UNC5C

Unc-5 netrin receptor C

VAMP1

Vesicle-associated membrane protein 1

VAMP5

Vesicle-associated membrane protein 5

VAPB

Vesicle-associated membrane protein B and C

VAT1

Vesicle amine transport 1

VGF

VGF nerve growth factor inducible

VPS35

Retromer complex component

VSNL1

Visinin-like protein 1

TMT proteomics

Data are available for 160 ROS and MAP participants.

Tandem mass tags are chemical labels used in tandem mass spectrometry to identify and quantify proteins and other macromolecules.